Physicochemical Correlation between Amino Acid Sites in Short Sequences under Selective Pressure. - David S. Campo; Zoya Dimitrova; Yuri Khudyakov (ISBRA, 2008)

Invited Keynote Talk: Integrative Viral Molecular Epidemiology: Hepatitis C Virus Modeling. - James Lara; Zoya Dimitrova; Yuri Khudyakov (ISBRA, 2008)

HCV Quasispecies Assembly Using Network Flows. - Kelly Westbrooks; Irina Astrovskaya; David S. Campo; Yuri Khudyakov; Piotr Berman; Alexander Zelikovsky (ISBRA, 2008)

Artificial neural network for prediction of antigenic activity for a major conformational epitope in the hepatitis C virus NS3 protein. - James Lara; Robert M. Wohlhueter; Zoya Dimitrova; Yuri Khudyakov (Bioinform., 2008)

Variation in physicochemical properties of the hypervariable region 1 during acute and chronic stages of hepatitis C virus infection. - Irina V. Astrakhantseva; David S. Campo; Aufra Araujo; Chong-Gee Teo; Yuri Khudyakov; Saleem Kamili (BIBM Workshops, 2011)

Network of coordinated substitutions in the Hepatitis B virus polymerase. - David S. Campo; Zoya Dimitrova; James Lara; Mike Purdy; Hong Thai; Sumathi Ramachandran; Lilia Ganova-Raeva; X. Zhai; Joseph C. Forbi; Chong-Gee Teo; Yuri Khudyakov (BIBM Workshops, 2011)

Assessments of intra- and inter-host diversity of hepatitis C virus using Next Generation Sequencing and Mass spectrometry. - Zoya Dimitrova; David S. Campo; Sumathi Ramachandran; Gilberto Vaughan; Lilia Ganova-Raeva; Yulin Lin; Joseph C. Forbi; Guo-liang Xia; Pavel Skums; Brian L. Pearlman; Yuri Khudyakov (BIBM Workshops, 2011)

Modeling antigenic property of the hepatitis C virus NS3 protein. - James Lara; Yuri Khudyakov (BIBM Workshops, 2011)

Host-specific HCV evolution and response to the combined interferon and ribavirin therapy. - James Lara; John E. Tavis; Maureen J. Donlin; William M. Lee; He-Jun Yuan; Brian L. Pearlman; Gilberto Vaughan; Joseph C. Forbi; Guo-liang Xia; Yuri Khudyakov (BIBM Workshops, 2011)

Modelling differential interferon resistance of HCV quasispecies. - Pavel Skums; David S. Campo; Zoya Dimitrova; Gilberto Vaughan; Daryl T. Lau; Yuri Khudyakov (BIBM Workshops, 2011)

Efficient error correction for next-generation sequencing of viral amplicons. - Pavel Skums; Zoya Dimitrova; David S. Campo; Gilberto Vaughan; Livia Rossi; Joseph C. Forbi; Jonny Yokosawa; Alex Zelikovsky; Yuri Khudyakov (BMC Bioinform., 2012)

Differences in variability of hypervariable region 1 of hepatitis C virus (HCV) between acute and chronic stages of HCV infection. - Irina V. Astrakhantseva; David S. Campo; Aufra Araujo; Chong-Gee Teo; Yuri Khudyakov; Saleem Kamili (Silico Biol., 2012)

Coordinated evolution of the Hepatitis B Virus Polymerase. - David S. Campo; Zoya Dimitrova; James Lara; Mike Purdy; Hong Thai; Sumathi Ramachandran; Lilia Ganova-Raeva; X. Zhai; Joseph C. Forbi; Chong-Gee Teo; Yuri Khudyakov (Silico Biol., 2012)

Evaluation of viral heterogeneity using next-generation sequencing, end-point limiting-dilution and mass spectrometry. - Zoya Dimitrova; David S. Campo; Sumathi Ramachandran; Gilberto Vaughan; Lilia Ganova-Raeva; Yulin Lin; Joseph C. Forbi; Guo-liang Xia; Pavel Skums; Brian L. Pearlman; Yuri Khudyakov (Silico Biol., 2012)

Association of antigenic properties to structure of the hepatitis C virus NS3 protein. - James Lara; Yuri Khudyakov (Silico Biol., 2012)

Coordinated evolution among hepatitis C virus genomic sites is coupled to host factors and resistance to interferon. - James Lara; John E. Tavis; Maureen J. Donlin; William M. Lee; He-Jun Yuan; Brian L. Pearlman; Gilberto Vaughan; Joseph C. Forbi; Guo-liang Xia; Yuri Khudyakov (Silico Biol., 2012)

Numerical detection, measuring and analysis of differential interferon resistance for individual HCV intra-host variants and its influence on the therapy response. - Pavel Skums; David S. Campo; Zoya Dimitrova; Gilberto Vaughan; Daryl T. Lau; Yuri Khudyakov (Silico Biol., 2012)

Mutational robustness of hepatitis C virus intra-host variants. - David S. Campo; Zoya Dimitrova; Pavel Skums; Yuri Khudyakov (ICCABS, 2013)

Hepatitis C virus genetic association to rate of liver fibrosis progression. - James Lara; Yuri Khudyakov; F. Xavier López-Labrador; Fernando González-Candelas; Marina Berenguer (ICCABS, 2013)

Computational analysis and modelling of intra-host adaptation of hepatitis C virus: The role of immune cross-reactivity of HCV quasispecies. - Pavel Skums; David S. Campo; Zoya Dimitrova; Leonid Bunimovich; Yuri Khudyakov (ICCABS, 2013)

Optimizing pooling strategies for the massive next-generation sequencing of viral samples. - Pavel Skums; Olga Glebova; Alex Zelikovsky; Ion I. Mandoiu; Yuri Khudyakov (ICCABS, 2013)

Alignment of DNA Mass-Spectral Profiles Using Network Flows. - Pavel Skums; Olga Glebova; Alex Zelikovsky; Zoya Dimitrova; David Stiven Campo Rendon; Lilia Ganova-Raeva; Yuri Khudyakov (ISBRA, 2013)

Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows. - Pavel Skums; Nicholas Mancuso; Alexander Artyomenko; Bassam Tork; Ion I. Mandoiu; Yuri Khudyakov; Alex Zelikovsky (BMC Bioinform., 2013)

New computational methods for assessing the genetic relatedness of close viral variants. - David S. Campo; Zoya Dimitrova; Guo-liang Xia; Pavel Skums; Lilia Ganova-Raeva; Yuri Khudyakov (ICCABS, 2014)

Detection of genetic relatedness between viral samples using EM-based clustering of next-generation sequencing data. - Pavel Skums; Alexander Artyomenko; Olga Glebova; Alex Zelikovsky; David S. Campo; Zoya Dimitrova; Yuri Khudyakov (ICCABS, 2014)

Computational models of liver fibrosis progression for hepatitis C virus chronic infection. - James Lara; F. Xavier López-Labrador; Fernando González-Candelas; Marina Berenguer; Yuri Khudyakov (BMC Bioinform., 2014)

Highlights: Predicting the cross-immunoreactivity of hepatitis C virus hyper-variable region 1 peptides using polynomial neural networks. - James Lara; Yury Khudyakov; Livia Rossi; Gilberto Vaughan (ICCABS, 2015)

Efficient detection of viral transmission with threshold-based methods. - Inna Rytsareva; Seth Sims; Sriram P. Chockalingam; Srinivas Aluru; David S. Campo; Cansu Tetik; Sharma V. Thankachan; Yury Khudyakov; Yueli Zheng; Chirag Jain; Amanda Sue (ICCABS, 2015)

Algorithms for prediction of viral transmission using analysis of intra-host viral populations. - Pavel Skums; Olga Glebova; David S. Campo; Nana Li; Zoya Dimitrova; Seth Sims; Leonid Bunimovich; Alex Zelikovsky; Yury Khudyakov (ICCABS, 2015)

Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling. - Pavel Skums; Alexander Artyomenko; Olga Glebova; Sumathi Ramachandran; Ion I. Mandoiu; David S. Campo; Zoya Dimitrova; Alex Zelikovsky; Yuri Khudyakov (Bioinform., 2015)

Modeling the functional state of the reverse transcriptase of hepatitis B virus and its application to probing drug-protein interaction. - Xiaojun Xu; Hong Thai; Kathryn M. Kitrinos; Guo-liang Xia; Anuj Gaggar; Matthew Paulson; Lilia Ganova-Raeva; Yury Khudyakov; James Lara (BMC Bioinform., 2016)

CAME 2017: 6th Workshop on Computational Advances in Molecular Epidemiology. - Yury Khudyakov; Ion I. Mandoiu; Pavel Skums; Alexander Zelikovsky (BCB, 2017)

Classification of HCV infections through sequence image normalization. - Sunitha Basodi; Pelin Burcak Icer; Pavel Skums; Yury Khudyakov; Alexander Zelikovsky; Yi Pan 001 (ICCABS, 2017)

Assessment of HCV infection stage as recent or chronic using multi-parameter analysis and machine learning. - Pelin Icer Baykal; Alexander Artyomenko; Sumathi Ramachandran; Yury Khudyakov; Alex Zelikovsky; Pavel Skums (ICCABS, 2017)

Efficient filtering algorithm for detection of genetic similarity between large genomic datasets. - Viachaslau Tsyvina; David S. Campo; Seth Sims; Alex Zelikovsky; Yury Khudyakov; Pavel Skums (ICCABS, 2017)

Agent-Based in Silico Evolution of HCV Quasispecies. - Alexander Artyomenko; Pelin B. Icer; Pavel Skums; Sumathi Ramachandran; Yury Khudyakov; Alex Zelikovsky (ISBRA, 2017)

Modeling the Spread of HIV and HCV Infections Based on Identification and Characterization of High-Risk Communities Using Social Media. - Deeptanshu Jha; Pavel Skums; Alex Zelikovsky; Yury Khudyakov; Rahul Singh (ISBRA, 2017)

ACM-BCB 2018 Computational Advances in Molecular Epidemiology (CAME) Chairs' Welcome. - Yury Khudyakov; Ion I. Mandoiu; Pavel Skums; Alexander Zelikovsky (BCB, 2018)

QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data. - Pavel Skums; Alex Zelikovsky; Rahul Singh; Walker Gussler; Zoya Dimitrova; Sergey Knyazev; Igor Mandric; Sumathi Ramachandran; David S. Campo; Deeptanshu Jha; Leonid Bunimovich; Elizabeth Costenbader; et al. (Bioinform., 2018)

Automated quality control for a molecular surveillance system. - Seth Sims; Atkinson G. Longmire; David S. Campo; Sumathi Ramachandran; Magdalena Medrzycki; Lilia Ganova-Raeva; Yulin Lin; Amanda Sue; Hong Thai; Alexander Zelikovsky; Yury Khudyakov (BMC Bioinform., 2018)

Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants. - Viachaslau Tsyvina; David S. Campo; Seth Sims; Alex Zelikovsky; Yury Khudyakov; Pavel Skums (BMC Bioinform., 2018)

Workshop on Computational Advances in Molecular Epidemiology. - Yury Khudyakov; Ion I. Mandoiu; Pavel Skums; Alexander Zelikovsky (BCB, 2019)

Convex hulls in hamming space enable efficient search for similarity and clustering of genomic sequences. - David S. Campo; Yury Khudyakov (BMC Bioinform., 2020)

SOPHIE: Viral Outbreak Investigation and Transmission History Reconstruction in a Joint Phylogenetic and Network Theory Framework. - Pavel Skums; Fatemeh Mohebbi; Vyacheslav Tsyvina; Pelin Icer; Sumathi Ramachandran; Yury Khudyakov (RECOMB, 2022)

Primary case inference in viral outbreaks through analysis of intra-host variant population. - Walker Gussler; David S. Campo; Zoya Dimitrova; Pavel Skums; Yury Khudyakov (BMC Bioinform., 2022)

A Novel Information-Theory-Based Genetic Distance That Approximates Phenotypic Differences. - David S. Campo; Alexander Mosa; Yury Khudyakov (J. Comput. Biol., 2023)

Tool-augmented LLMs as a Universal Interface for IDEs. - Yaroslav Zharov; Yury Khudyakov; Evgeniia Fedotova; Evgeny Grigorenko; Egor Bogomolov (IDE@ICSE, 2024)

Special Section: 12th International Computational Advances in Bio and Medical Sciences (ICCABS 2023). - Mukul S. Bansal; Wei Chen; Yury Khudyakov; Ion I. Mandoiu; Marmar Moussa; Murray Patterson; Sanguthevar Rajasekaran; Pavel Skums; Sharma V. Thankachan; Alex Zelikovsky (J. Comput. Biol., 2025)